Phylogenetics, Biogeography, and Patterns of Diversification Of
Total Page：16
File Type：pdf, Size：1020Kb
Brigham Young University Masthead Logo BYU ScholarsArchive All Theses and Dissertations 2017-04-01 Phylogenetics, Biogeography, and Patterns of Diversification of GeckosAcross the Sunda Shelf with an Emphasis on the GenusCnemaspis (Strauch, 1887) Perry Lee Wood Brigham Young University Follow this and additional works at: https://scholarsarchive.byu.edu/etd BYU ScholarsArchive Citation Wood, Perry Lee, "Phylogenetics, Biogeography, and Patterns of Diversification of GeckosAcross the Sunda Shelf with an Emphasis on the GenusCnemaspis (Strauch, 1887)" (2017). All Theses and Dissertations. 7259. https://scholarsarchive.byu.edu/etd/7259 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in All Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Phylogenetics,Biogeography,andPatternsofDiversificationofGeckos AcrosstheSundaShelfwithanEmphasisontheGenus Cnemaspis(Strauch,1887) PerryLeeWood Jr. Adissertationsubmittedtothefacultyof BrighamYoungUniversity inpartialfulfillmentoftherequirementsforthedegreeof DoctorofPhilosophy JackW.Sites Jr.,Chair ByronJ.Adams SethM.Bybee L.LeeGrismer DukeS.Rogers DepartmentofBiology BrighamYoungUniversity Copyright©2017PerryLeeWood Jr. AllRightsReserved ABSTRACT Phylogenetics,Biogeography,andPatternsofDiversificationofGeckos AcrosstheSundaShelfwithanEmphasisontheGenus Cnemaspis(Strauch,1887) PerryLeeWood Jr. DepartmentofBiology,BYU DoctorofPhilosophy InmydissertationIinvestigatetwogeneraofgeckos(CyrtodactylusandCnemaspis)thatare distributedacrossSoutheastAsiawithanemphasisonCnemaspis. InChapter1Iuseamulti- locusdataset,ancestralareaanalyses,andmolecularclockdatingtogenerateaspeciesleveltime calibratedphylogenytotestthemonophylyofCyrtodactylusandtoidentifymajorbiogeographical patterns. IidentifiedthatCyrtodactylusismonophyleticonlyifthetheSriLankangenusoften recognizedasGeckoellaisincluded. TheresultsoftheBiogeographicalanalysesrevealawestto eastpatternofdiversification.Chapter2Iuseatraditionalmorphologicaldatasettodescribeanew speciesofCnemaspisfromPeninsularMalaysia. InChapter3mycolleaguesandIuseamulti- locusdatasetandmorphologicalcharacterstorevisethetaxonomyofallCnemaspisspeciesand putthisinaphylogeneticcontext.Thisresultedinthedescriptionofeightnewspeciesandallowed ustogeneratehypothesesrelatingtoparallelevolution,diversity,andbiogeography.InChapter4I useadditionaltaxonsamplingofCnemaspisfromThailandtogenerateamorecompletephylogeny and use an integrative taxonomic approach to describe three new species. In Chapter 5 I used highthroughputsequencingofsequencecaptureandUltraConservedElementstotestforarapid radiationinCnemaspisandtoinvestigatebiogeographichypothesesrelatingtothediversification andevolutionofCnemaspis.IdeterminedthattherewasatemporalrapidradiationofCnemaspis thatcoincideswiththetemporaldiversificationofotherterrestrialvertebratesacrossSundaland. The results of these studies indicate that the species diversity of Cnemaspis is underestimated andthatbothgenerahaveexperiencedsimilartemporalandspatialdiversificationcoincidingwith majorvicarianteventsduringtheEoceneandtheOligocene-Miocenetransition. Keywords:biogeography,Cnemaspis,Cyrtodactylus,evolution,SoutheastAsia,taxonomy,ultra conservedelements ACKNOWLEDGMENTS I would like express many thanks to the graduate students at BYU, the department of biol- ogy (especially, Gentri Glaittli, Justina Tavana, and Dennis Shiozawa), and my committee (Byron Adams, Seth Bybee, Duke Rogers, Lee Grismer, and Jack Sites) for helping me along the way. I would like to highlight a special thanks to my amazing and patient advisor, Jack Sites. He spent numerous hours and late nights/early mornings editing my manuscripts and making sure that I had everything I needed to excel and grow as a “great” graduate student at BYU. The funding for mul- tiple research trips and meetings was greatly appreciated, too. I am also grateful for my friend and colleague Lee Grismer who has been putting up with me for 16 years starting from a punk kid (un- dergraduate) to a graduate student and many years of field work together all over the world. I am grateful for the graduate students in the Site’s lab (César Aguilar, Derek Tucker, Luke Welton) and past students, post-doc Juan Santos and his wife Natalia Biani, and visiting researchers Mariana Morando and Luciano Avila for many hours of conversations about research projects and normal day life. Thank you also to the people at the University of Washington (Adam Leaché, Jamie Oaks, Leonard Jones, Itzue Caviedes-Solis, Nassima Bouzid, and Matt McElroy) for mentorship and emotional support while generating genomic data. I would like to acknowledge friends and colleagues Dan Portik and Phillip Skipwith, who provided advice and helpful discussions of phy- logenetic software. Special thanks to my international colleagues and friends, Evah Quah, Shahrul Anuar, and Anchalee Aowphol (and their students) for sharing their love of science, great food, and hard work in the field. My family and friends for always being there for me regardless of the situation. Lastly, my wife, Margaret, and my dog, Cloe, for putting up with me for leaving them all the time to go into the field multiple times a year. I could not do this without your unconditional love, support, and encouragement. Table of Contents Title Page…………………………………………………………………………………………..i Abstract……………………………………………………………………………………………ii Acknowledgments………………………………………………………………………………..iii Table of Contents……………………………………………………………………………..iv–vii List of Tables………………………………………………………………………………...viii–ix List of Figures………………………………………………………………………………...x–xiv Chapter 1: Phylogeny of bent-toed geckos (Cyrtodactylus) reveals a west to east pattern of diversification…………………………………………………………………………………1–13 Abstract……………………………………………………………………………………2 Introduction……………………………………………………………………………..2–3 Materials and Methods………………………………………………………………….3–7 Taxon sampling, data collection, and sequence alignment………………………..3 Phylogeny reconstruction……………………………………………………….3–6 Divergence timing and ancestral area analyses………………………………...6–7 Results…………………………………………………………………………………..7–9 Discussion……………………………………………………………………………..9–12 Phylogeny……………………………………………………………………..9–10 Biogeography………………………………………………………………...10–11 Taxonomy……………………………………………………………………11–12 Conclusions………………………………………………………………………12 Acknowledgements………………………………………………………………………12 References……………………………………………………………………………12–13 Chapter 2: A new species of lowland karst dwelling Cnemaspis Strauch, 1887 (Squamata: Gekkonidae) from northwestern Peninsular Malaysia………………………………………14–35 Abstract…………………………………………………………………………………..15 Introduction………………………………………………………………………………15 Materials and Methods……………………………………………………………….17–18 Systematics…………………………………………………………………………..18–33 Discussion………………………………………………………………………………..33 Acknowledgments……………………………………………………………………….33 References……………………………………………………………………………33–34 Appendix……………………………………………………………………………..34–35 Chapter 3: Systematics and natural history of Southeast Asian Rock Geckos (genus Cnemaspis Strauch, 1887) with descriptions of eight new species from Malaysia, Thailand, and Indonesia……………………………………………………………………………………36–183 Abstract…………………………………………………………………………...……...40 Introduction……………………………………………………………………...…..40–42 Materials and Methods……………………………………………………………….42–51 Molecular Analysis…………………………………………………………..42–43 Phylogenetic Analysis……………………………………………………………43 Morphological Analysis……………………………………………………...43–50 iv Species Accounts………………………………………………………………...51 Results……………………………………………………………………………....51–173 Taxonomy………………………………………………………………....……..58 Ca Mau Clade………………………………………………………………..58–62 Cnemaspis boulengerii………………………………………………59–60 Cnemaspis psychedelica……………………………………………..60–62 Pattani Clade…………………………………………………………………62–75 Cnemaspis monachorum………………………………………….….63–70 Cnemaspis biocellata………………………………………………...70–72 Cnemaspis niyomwanae………………………………………….…..72–74 Cnemaspis kumpoli…………………………………………………..74–75 Northern Sunda Clade..……………………………………………………..75–132 Chanthaburiensis Group…………………….……………………….76–95 Cnemaspis chanthaburiensis……….................……………..76–78 Cnemaspis neangthyi…………………………………….......78–79 Cnemaspis aurantiacopes…………………………………....79–80 Cnemaspis caudanivea……………………………………….80–82 Cnemaspis nuicamensis……………………………………...82–83 Cnemaspis tucdupensis……………………………………....84–85 Cnemaspis siamensis………………………………………...85–86 Cnemaspis huaseesom……………………………………….87–88 Cnemaspis chanardi………………………………………….88–90 Cnemaspis omari sp. nov…………………………………….90–94 Cnemaspis roticanai…………………………………………94–95 Argus Group………………………………………………………...96–102 Cnemaspis flavigaster………………………………………..96–97 Cnemaspis argus……………………………………………..98–99 Cnemaspis karsticola…………………………………………….99 Cnemaspis perhentianensis………………………………..100–102 Affinis Group………………………………………………………102–132 Cnemaspis affinis………………………………………….102–104 Cnemaspis harimau……………………………………….104–106 Cnemaspis pseudomcguirei……………………………….106–108 Cnemaspis shahruli………………………………………..108–110 Cnemaspis mcguirei……………………………………….110–114 Cnemaspis grismeri……………………………………….114–116 Cnemaspis flavolineata……………………………………116–117 Cnemaspis temiah sp. nov…………………………………117–121 Cnemaspis narathiwatensis……………………………….121–122 Cnemaspis hangus sp. nov………………………………...122–126 Cnemaspis selamatkanmerapoh………………………………...126 Cnemaspis bayuensis……………………………………...126–128 Cnemaspis stongensis sp. nov………………………..……129–132 Southern Sunda Clade……………………………………………………..133–161 Cnemaspis